[CIG-MC] PBS batch configurations

Leif Strand leif at geodynamics.org
Tue Oct 27 13:44:14 PDT 2009

Hi Rob,

There is an example PBS file on this page:


Based on the information you gave, your CitcomS.cfg file should look 
like the following:

scheduler = pbs

command = mpirun -np ${nodes} -hostfile ${PBS_NODEFILE}

ppn = 8  ; processors per node

You can set the job name and walltime from the command line:

     citcoms --job.name=test --job.walltime=1*hour [...]

Or, from a .cfg file:

walltime = 1*hour
name = test

To debug the PBS settings, use "--scheduler.dry":

     citcoms --scheduler.dry

This will dump the script to the terminal, instead of actually 
submitting it.


Robert Moucha wrote:
> Hi All,
> I'm using a new cluster that uses the MOAB pbs scheduler, our previous
> cluster did not use a batch system. I am trying to figure out how to
> set the parameters in CitcomS.cfg, in the manual only lsf settings are
> shown.  In particular, how do I specify multiple special options for
> pbs. Is the following cfg file correct for the launch script below?
> Or, does any one have a sample cfg file for pbs?
> [CitComS]
> scheduler = pbs
> [CitcomS.pbs]
> pbs-options = [-N test, -l nodes=2:ppn=8,walltime=1:00:00]
> [Citcoms.launcher]
> command = mpirun
> Here is an example of a batch submission script that is used on the cluster:
> #!/bin/bash
> # MOAB/Torque submission script for SciNet GPC (ethernet)
> #
> #PBS -l nodes=2:ppn=8,walltime=1:00:00
> #PBS -N test
> # DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
> # EXECUTION COMMAND; -np = nodes*ppn
> mpirun -np 16 -hostfile $PBS_NODEFILE ./a.out
> Thanks all,
> Rob

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